Skepticism

EVENTS

A questions about those ancient bacterial fossils…

Both Jerry Coyne and Larry Moran have good write-ups on the recent discovery of what are purportedly the oldest fossil cells, at 3.4 billion years old. I just have to add one little comment: a small, niggling doubt and something that bugs me about them. All the smart guys are impressed with this paper, but this one little thing gives me pause.

I’m a microscopist — I look at micrographs all the time, and one of the things I always mentally do is place the size of things in context. And I was looking at the micrographs of these fossils, and what jumped out at me is how large they are. They’re not impossibly large, they’re just well out of the range I expect for prokaryotes.

Most prokaryotes have diameters in the range of 1-10µm, while typical eukaryotes are about 10 times that size. There are exceptions: Thiomargarita gets up to 500µm across, so like I say, there’s nothing impossible about these cells, it’s just that the micrographs show lots of cells with 10-30µm diameters. And the authors come right out and report that:

The size range is also typical of such assemblages, with small spheres and ellipsoids 5–25 µm in diameter, rare examples (<10) of larger cellular envelopes up to 80 µm in diameter, and tubes 7–20 µm across (see ref. 24).

How odd. When I poke into the nervous system of an embryonic insect or fish, those are the sizes of cells I often see (well, except there aren’t many tubes of that size!). When I poke into a culture or embryo contaminated with bacteria, they’re much, much smaller. So maybe paleoarchaean bacteria tended to be larger? And they do cite a source for that size range of prokaryotes…

Then here’s a new problem: the source cited, ref. 24, is the Schopf paper, the older paper that claimed to have found ancient bacterial fossils, a claim that has since been discredited! Uh-oh. What they’re calling “typical of such assemblages” is a data set that’s widely considered artifactual now. Furthermore, that’s a simplified version of what Schopf said — he actually broke the sizes down into categories, and the range was more like 1-30 µm.

So Schopf was reporting larger cells in his older samples, and now Wacey et al. are describing what look like very large cells to me in their 3.4 billion year old rocks. I’m not a microbiologist so I could be way off on this, but…isn’t this just a little bit strange? Maybe there are some micro people out there who can reassure me that this isn’t a surprising result.

For no particular reason at all (everything I know about biology I’ve learned from the internet), when you said the cells were larger than you expected, it struck me as quite plausible that early prokaryotes would be larger than their modern descendants. Maybe more specialized organelles hadn’t evolved yet, so a smaller set of organelles and processes had to do all the necessary jobs. This would likely take up more room.

An example from computing: a special purpose video encoder is much smaller than a general-purpose CPU that could do the same job.

I guess my point is, how much like modern organisms should we expect primitive microbes to be?

Well, not at all a microbio person, but it strikes me as not particularly odd that you would have larger cell sizes in an archetypal prokaryote than in the modern version. Assuming that there is some selective pressure to divide faster (and therefore at a smaller size if anabolism is rate limited), larger-than-modern prokaryotes seem plausible. Of course, plausible is hardly supportive evidence…

I remember the earlier study, and that it was decided the results were not organic. There also a claim about fossil bacteria in a meteorite from Mars, although these were supposed to be far smaller than typical Terran bacteria.

Still, this is a good example of the scientific process at work. Put your results out there and let the scientific community take pot shots at it. If it survives, the hypothesis is stronger from the scrutiny. Quite different from the way religion handles data that contradicts cherished beliefs.

If you’re right, and they’re really citing discredited research, I’d call that more than just a “small, niggling doubt.” I’d call that a damn good reason to reconsider their conclusions and wait for more evidence to emerge.

Okay, so picking nits here, but it’s possible to gather a lot of good data and have your conclusions regarding that data go down the tank.

While it was ultimately found that the particular alleged microfossils studied in that paper didn’t stand up as microfossils and appear to have developed inorganically, does that mean that when those earlier authors said in their paper that this is the size range to be expected that they were also automatically wrong about the size range? Or could it be that they were right about the size range…which is part of what fooled them into thinking that those patterns were fossils?

Like most other folk here, I know next to nothing about taphonomy and microbiology, but I’d be wary of throwing out a piece of evidence used in one line of an argument because it turns out that the argument as a whole wasn’t sound…

I am certainly with PZed on being skeptical about the identification, however. Not knowing how they ID microfossils as definitively organic and being familiar with famous cases in which bright, knowledgeable people said they saw fossils and turned out to be either wrong or premature (ware the confirmation bias!) I was dubious when I saw this study.

I’m excited, don’t get me wrong. And I think the evidence is really, really strong that life was going well by about 2.4 billion years ago (Great Oxidation Event and precursors nail that one down), they existence of cyanobacteria no later than 2.15 Ga isn’t enough that I’m certain that we must have had heterotrophs by 3.4 Ga. I wouldn’t be surprised, but I’m not convinced.

So I really, really want more from this as well. Exactly what is considered a “smoking gun” that a particular pattern was produced organically or at least taphonomically? Was a smoking gun found here? If not, what was the evidence that convinced the team? What was different between their sample and the sample that they attacked as inorganic a few years ago? … a sample, I might add, that was taken from the same geological formation not far distant from the one this new team is now embracing…

#20 Crip Dyke
I guess a partial answer to your questions might be Jerry Coyne’s puzzled observation that “this finding certainly deserves a berth in the very highest-profile journals,” i.e. not Nature Geosciences. Just speculation, but Nature may have received it first, then sent it to Nature Geosciences because of the lack of a smoking gun. With the earlier work being discredited, it probably raises the ante quite a bit…
But, yeah, I too would like to know of some rigid criterion – like the 5 sigma threshold in particle physics – that helps distinguish the true fossils.

Oh, look! Mythusmage, an old time troll, has come back in order to talk out of his ass. And he did not disappoint. He added nothing. Just drooled about an old myth that had nothing to do with the topic.

The large modern day prokaryotes cited in #18 seem to be very strucurally specialised to overcome the problem of their large volume to surface area ratios (IIRC, prokaryotic respiration occurs across the cell membrane so cells are limited to be small in order to be able to respire adequately). Is there any evidence of such structural adaptation in these fossils or are they small enough not to worry?

does that mean that when those earlier authors said in their paper that this is the size range to be expected that they were also automatically wrong about the size range? Or could it be that they were right about the size range

I don’t follow your logic. Of course they were likely right about the size range of what they were studying, but if what they were studying wasn’t organic, what possible relevance can the size range have to microfossils?

In response to the “seems find to me” messages: There was at least half a billion years before eukaryotes started to get themselves running. Now with it just being prokaryotes for all that time it is a little bit strange to think that the cells rarely ever reach that size even though early ones were like that. Maybe they did just get flat out out-competed really quickly but I don’t know that there’s enough here to say there’s good reason to support that.

*I’ve only got a BS in Biology but it was a fairly chemistry and microbiology based program. Definitely no authority on this in particular but that’s my reasoning for why the criticism is warranted.

well what I want to know is what was the atmosphere of the planet like ate that time? what was the environment that these things were growing in like.

Hot volcanic mod rich in sulfur? no or very little free O2 high ozone levels? high radiation?
what would the storms be like? was there a deep sea or a shallow one on which the storms could feed?
one thing is clear we are pushing on the beginning. If it is not the beginning it is what the first life stuff here saw. What ever these structures are we will eventually get them figured out with out much doubt.
its fun watching it happen

@Pepijn #33
Well…Depends if you’re being an idiot on purpose and dicking with us.
I’m not a biologist so this is based on my knowledge… The thing about evolution is that it isn’t arbitrary. Due to the high mutation rate in prokaryotes and the immense amount of time, there is likely a selective pressure toward smaller size. It’s also possible that there hasn’t been a selective pressure toward size, though the relative difference of the fossilized cells and the cells common today makes that slightly more unlikely. I think a more likely explanation for this phenomenon (if it is a consistent trend) either has something to do with the fossilization process and/or geologic processes OR it has something to do with the environment of the time in which these cells came from (levels of carbon dioxide, oxygen, sulfur dioxide, nitrogen, etc.).

Probably too much for the question, but I figure that I may as well. Feel free to correct me if I’m wrong.

If these really are bacterial fossils then they are the size they are.

There is no need to try to generalise about ancient prokaryotes on the basis of a single example, given that this would represent the only species discovered from that period.

If Brachiosaurus was the only known example of Dinosauria, then it would be misleading to generalise that all such species were large and therefore for whatever particular reason. That these putative fossils are large but well within the size range of known prokaryotes says very little about their status as microfossils. They may be an outlier in terms of size, or they may be representative, but it is impossible to know.

Other diagnostic features are more important than size. It is argued that the biogenicity of these samples is supported by a number of observations, including the narrow distribution of cell (recognising that such an identifier is only putative) size, consistent cell wall thickness, and gross and colonial morphologies similar to other microfossils and modern prokaryotes. Additionally, the authors claim that the features are inconsistent with alternative geochemical explanations.

I’m not a microbiologist, but I have a fair amount of experience in unicellular eukaryotic and prokaryotic cell biology, and I can’t really see any reason to take a view based on size alone. Unfortunately, I’m in no way equiped to make a judgement on the basis of the geochemistry and more specialised microfossil evidence. The evidence presented in the micrographs and statistical treatments of morphological data appear to be consistent with large prokaryotic cells, but there may be alternative interpretations about which I’m not qualified to make judgements.

When I poke into a culture or embryo contaminated with bacteria, they’re much, much smaller.

This is rather misleading – common laboratory contaminants come from a relatively narrow range of ubiquitous aerobic bacteria which can grow in very generalised environments. They will probably be dividing in the relatively rich environment, they will be competing for nutrients, and will therefore be the smaller species with a short doubling period.

Most prokaryotes are not culturable or require very specialised culture conditions. The few that you see are not broadly representative of prokaryotic morphology. Certainly, you will not see psychrophilic or aerobic bacteria, and none of the sulphur-reducing bacteria.

Bernard Bumner: Sorry dude but the paper made the claim that this size was typical. Their citation for that isn’t any good so we are all essentially arguing the same point: these shouldn’t be treated like they are typical.

It is possible that the bacteria in question were preferentially selected for by conditions. Thus the smaller bacteria were selected against by local conditions, leaving the field, as it were, open to the larger bacteria.

Then too there is the absence of eukaryotes to consider, which would leave niches to prokaryotes, and may even have made other niches possible, niches later ‘closed off’ by the rise of nucleated cells.

To better explain my thinking, local conditions selected for the preservation of large bacterial remains, and selected against the preservation of small deceased bacteria. I hope that makes things clearer.

Sorry dude but the paper made the claim that this size was typical. Their citation for that isn’t any good so we are all essentially arguing the same point: these shouldn’t be treated like they are typical.

Well, it isn’t necessarily that the citation isn’t any good, it is that the citation contains some good and some not so good information. The Schopf paper reviews various microfossil assemblages, only some of which appear to have been discredited (which is probably the wrong word to use). The specific claim for the discovery of the oldest microfossils in the Schopf paper is apparently agreed by a majority to be incorrect (although not by the author, and the consensus is seemingly not settled on the matter).

The claim in the new paper is not about absolute size, but that the size range is typical of such assemblages, which even if true really says little about early prokaryotes generally (given the paucity of ancient microfossil evidence). I was in no small part cautioning against making general arguments about ancient prokaryotes being larger than modern species. When dealing with fossil evidence it is always important to remember that you are probably observing something that is poorly representative of the full diversity of species, since the conditions required for fossilisation are quite rare and often poorly understood.

My other contention is that size alone cannot discredit these specimens as microfossils, since their size may be remarkable (or not). There are much more important diagnostic features which seem to support the identification of these features as microfossils. That is why the claims have been better received than Schopf’s – this paper uses a greater range of methods to test the putative biogenic remains.

Crip Dyke, Right Reverend Feminist FuckToy of Death & Her Handmaidensays

does that mean that when those earlier authors said in their paper that this is the size range to be expected that they were also automatically wrong about the size range? Or could it be that they were right about the size range

I don’t follow your logic. Of course they were likely right about the size range of what they were studying, but if what they were studying wasn’t organic, what possible relevance can the size range have to microfossils?

No. I didn’t say that they might be right about the size range of what they studied. I said they might be right about the size range ***to be expected***

When I said that, I meant “to be expected of genuine fossils”.

They can be right not only about the size of what they studied, but that genuine microfossils can be expected to most commonly exhibit a certain size range, if dating from a given period. If they are right about that, they could be right about an entire line of argument, e.g. “these things are the right size to be genuine fossils, thus this is evidence that they are genuine fossils”.

Being right about a line of argument doesn’t mean that your entire argument is ultimately correct/sound.

Thus a paper can be a good source to cite for information about the size of genuine microfossils while being a bad source to cite for information about whether a particular rock actually contains microfossils.

This is the point I was trying to make. The paper isn’t necessarily a bad cite b/c they weren’t citing the paper to prove what was found, in that paper, to be unproven.

Okay, I was happy with everything up until that last sentence. I know what I’m saying. I hope it comes through.

Perhaps one last bit:

Scientist publishes a paper that declares this green 3′ by 3′ thingamabob to be the biggest leaf ever. Turns out is was siding from house that was blown off during a hurricane. Along the way, in the course of the paper, the scientist argues, “genuine leaves should ordinarily be green – although there are exceptions, this should be taken into consideration.”

The scientist can be wrong about the conclusion – this green thing is a leaf – while being right that we should expect, because of evolution & common descent providing uniformity in chlorophyl photosynthesis, leaves to be green.

A scientist later citing his paper to say that one characteristic of a leaf is that it has a high likelihood to be green isn’t using poor judgement. That argument was correct.

Does this make sense, JFD?

Crip Dyke, Right Reverend Feminist FuckToy of Death & Her Handmaidensays

I’ve come to understand that prokaryotes don’t, in fact, have organelles. I stand corrected.

Not quite. What they generally don’t have are organelles bounded by a lipid bilayer. They don’t have the complex endomembrane structures like those found in eukaryotes, in the form of organelles such as the nucleus, the golgi apparatus, and the endoplasmic reticulum.

Prokaryotes do have some internal compartmentalisation, and bounded internal organelles (usually with a lipid monolayer, like lipid bodies, the carboxysomes, PHB storage granules, or gas vacuoles). Just to complicate things, a few prokaryotes do have specialised organelles bounded by lipid bilayers, like photosynthetic membranes or magnetosomes.

Am I understanding correctly that only the latter of your examples is properly called an organelle?

It is a semantic debate, and one which isn’t really settled. There are plently of papers which make the argument that prokaryotic organelles really are just that, and the reason for it is very relevant to your second question:

I also get the impression the function of these organelles is somewhat simpler that the sort of stuff a typical organelle in a eukaryotic cell would do.

Simple is problematic once you reduce these sytems to a biochemical level – there is only more complexity in terms of the numbers of different reaction types and the size of the networks that occur in eukaryotic cells.

Ultimately, organelles simply operate as compartments, with additional functionality provided by their membranes and accosiated proteins. So the compartments may serve to establish differential concentrations of specific molecules, and the membrane may provide an additional property (like being hydrophobic) in order to set up, say, and electrochemical gradient to drive a specific type of reation.

This is true at a molecular level for both prokaryotic and eukaryotic systems, even though the latter are more complex. It is better to describe the prokaryotic system as more primative; i.e. coming first, the functionality from which eukaroytic systems are ultimately derived.

So I would accept the argument that eukaryotic and prokaryotic organelles are really distinguished by their type and by their biochemical composition, but that their functions are essentially similar at a molecular level.